All skills & plugins / Scientific Agent Skills (K-Dense)

pacsomatic

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.

Type: Skill by Beifang Niu
Catalog: Scientific Agent Skills (K-Dense)
Source: K-Dense-AI/scientific-agent-skills/skills/pacsomatic (7 files scanned)
Install and details: Agent Skills Index entry
License: MIT (LICENSE file)
Signals: Bundled scriptsSpawns processes

Pre-approved tools

No allowed-tools or tools list in its SKILL.md, command or agent files, so the agent asks before using tools as usual.

Hooks

No hooks.

MCP servers and apps

None.

Bundled code

1 code file (Python):

pacsomatic/scripts/run_pacsomatic.py

Network calls

No HTTP or socket call pattern found in the code.

Starts other programs

1 file. First match per file:

skills/pacsomatic/scripts/run_pacsomatic.py:76

completed = subprocess.run([java, "-version"], capture_output=True, text=True, timeout=30)

Credentials referenced

No key, token or secret environment variable found in code or MCP config.

Static scan of commit 5f2bc03 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.